The most common reasons for creating a custom linker script are to add custom linker section mappings, or additional memory regions. Both of these functions are available within the Nios® II BSP Editor, available by right-clicking on the BSP project within Eclipse, and selecting Nios II -> BSP Editor, and then selecting the "Linker Script" tab.
If the user requires aspects of a linker script that are not available in the gui, then the linker script generated by the BSP GUI cannot be used. After hand-creating the custom linker script, save this file locally to your software project, and then open the Makefile for editing. Locate the Makefile line that has a blank assignment for the variable "LINKER_SCRIPT" and complete the line to point to your custom script. After saving the makefile, this linker script will be used for future builds of your software.